Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.55 kDa 
• Atom Count: 3094 
• Modelled Residue Count: 363 
• Deposited Residue Count: 371 
• Unique protein chains: 2

3AMB

Protein kinase A sixfold mutant model of Aurora B with inhibitor VX-680

• DOI: 10.2210/pdb3AMB/pdb

• Classification: TRANSFERASE/TRANSFERASE inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-08-18 Released: 2011-08-03 
• Deposition Author(s): Pflug, A., de Oliveira, T.M., Bossemeyer, D., Engh, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.256 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Literature

Mutants of protein kinase A that mimic the ATP-binding site of Aurora kinase

Pflug, A., de Oliveira, T.M., Bossemeyer, D., Engh, R.A.

(2011) Biochem J 440: 85-93

• PubMed: 21774789 
• DOI: 10.1042/BJ20110592
• Primary Citation of Related Structures:  
  3AMA, 3AMB


• PubMed Abstract: 
  

We describe in the present paper mutations of the catalytic subunit α of PKA (protein kinase A) that introduce amino acid side chains into the ATP-binding site and progressively transform the pocket to mimic that of Aurora protein kinases. The resultant PKA variants are enzymatically active and exhibit high affinity for ATP site inhibitors that are specific for Aurora kinases. These features make the Aurora-chimaeric PKA a valuable tool for structure-based drug discovery tasks. Analysis of crystal structures of the chimaera reveal the roles for individual amino acid residues in the binding of a variety of inhibitors, offering key insights into selectivity mechanisms. Furthermore, the high affinity for Aurora kinase-specific inhibitors, combined with the favourable crystallizability properties of PKA, allow rapid determination of inhibitor complex structures at an atomic resolution. We demonstrate the utility of the Aurora-chimaeric PKA by measuring binding kinetics for three Aurora kinase-specific inhibitors, and present the X-ray structures of the chimaeric enzyme in complex with VX-680 (MK-0457) and JNJ-7706621 [Aurora kinase/CDK (cyclin-dependent kinase) inhibitor].

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Organizational Affiliation: 

Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase catalytic subunit alpha	A	351	Homo sapiens	Mutation(s): 6  Gene Names: PRKACA, PKACA EC: 2.7.11.11
UniProt & NIH Common Fund Data Resources
Find proteins for P17612 (Homo sapiens) Explore P17612  Go to UniProtKB:  P17612
PHAROS:  P17612 GTEx:  ENSG00000072062

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase inhibitor alpha	B	20	Homo sapiens	Mutation(s): 0  Gene Names: PKIA, PRKACN1
UniProt & NIH Common Fund Data Resources
Find proteins for P61925 (Homo sapiens) Explore P61925  Go to UniProtKB:  P61925
PHAROS:  P61925 GTEx:  ENSG00000171033

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VX6 (Subject of Investigation/LOI)	C [auth A]	CYCLOPROPANECARBOXYLIC ACID {4-[4-(4-METHYL-PIPERAZIN-1-YL)-6-(5-METHYL-2H-PYRAZOL-3-YLAMINO)-PYRIMIDIN-2-YLSULFANYL]-PHENYL}-AMIDE C23 H28 N8 O S GCIKSSRWRFVXBI-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Binding Affinity Annotations
ID	Source	Binding Affinity
VX6	Binding MOAD:  3AMB	Ki: 660 (nM) from 1 assay(s)
	PDBBind:  3AMB	Ki: 660 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.256 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.75	α = 90
b = 75.24	β = 90
c = 80.39	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2010-08-18 
• Released Date: 2011-08-03 
Deposition Author(s): Pflug, A., de Oliveira, T.M., Bossemeyer, D., Engh, R.A.

Revision History  

• Version 1.0: 2011-08-03
  Type: Initial release
  
• Version 1.1: 2011-09-07
  Changes: Structure summary
• Version 1.2: 2011-12-07
  Changes: Database references